Instantiation always creates error markers

[lwrage]

There should be a way to invoke instantiation without creating error markers on the instance model file.

child of #1018
needed by #603

[lwrage]

So far we have an additional entry point that records errors instead of adding markers. This can be used for tests. We still need to update the other entry points.

[lwrage]

There is no need to always save the instance model file.

[lwrage]

The remaining work will be done under #603